1. Conservation Genetics
Sam Hopkins
Biodiversity and Conservation Biology
An Optional Graphic
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2. What is conservation genetics?
Conservation genetics includes:
Study of inbreeding in small populations
Study of spatial patterns of genetic variation
Study of gene flow
Study of hybridisation
Study of systematics
Can start to describe the future of an endangered species
Can involve endangered taxa but often just species that will show us how something works
Genetics alone will not conserve species
So to start off, what is conservation genetics? It includes a number of different questions that can be answered with knowledge of genetics. Some of these types of studies are; studies of inbreeding in small populations, studies of genetic variation in space, studies of gene flow, studies of hybridisation and studies of systematics. Conservation genetics can also describe potential futures of an endangered species. This list is by no means complete. Conservation genetics can answer questions about endangered species but is often concerned with species that will answer a particular conservation genetics question. I must just stress that conservation genetics will not form conservation strategies alone many other factors have to be taken into consideration.

3. What is conservation genetics?
Conservation genetics allows conservationists to make informed decisions
Conservation genetics not always the answer
Its expensive
Time consuming
Interpretation is personal
Over all, conservation genetics allows conservationists to make more informed decisions, as with everything, the more knowledge we have the better choices we can make. However, it is not the definitive answer, it is expensive and time consuming and can hinder projects with a delay in definitive results. The results of each genetic analysis are subject to personal interpretation. I am now going to give some examples of how genetics is useful in conservation.

4. Conserving Humpback Whales 1
Depleted by hunting
Small populations survive in the North Atlantic, North Pacific and Southern Oceans
Separation between populations in different oceanic basins
Separation between populations in the same oceanic basin
Geographic variation studied by looking at the mitochondrial DNA
This study gives information on the Humpback but also may give insight into other species with high dispersal abilities, large distributions and social behaviours
The Humpback Whales were one of the many whale species that were hunted but are now protected. Small populations of Humpbacks still survive in the North Atlantic, North Pacific and Southern Oceans. The Humpback whales are split into 3 stocks due to land masses, the splits are between the North Atlantic, North Pacific and South Oceans. In addition to this there is some kind of separation within these stocks. For example, in the North Pacific, there is a group that feed around Alaska and winter in Hawaii and a group that feeds off California and winters in Mexico. This has been noted by observing naturally marked Whales and is suggested that animals rarely swap groups or migration patterns. However, the song of the Whales of the two populations is very similar each year even though it changes each year which suggests some communication between groups. A study of the geographical variation in the mitochondrial DNA was carried out. This gave an insight into the maternal line which is particularly important for animals like humpback whales where migration is possibly learnt from the mother. In the North Pacific the results showed a difference between the Alaskan and Californian populations and a connection between Alaskan and Hawaiian populations. The wintering grounds in Mexico were found to have connections to both the feeding grounds. The feeding ground seem to be the place where the populations split. In the southern ocean there are thought to be 5 or 6 different feeding groups. One of these groups migrates around the Eastern coast of Australia, one around New Zealand and another around the Western coast of Australia. Genetically the Eastern Australia and New Zealand groups were similar but there was a difference between these two groups and the group that migrates around Western Australia. In the North Atlantic the groups are split into east and west. The Western groups all breed and calve in the West Indies and then move to four different feeding grounds, Iceland, western Greenland, Newfoundland and the Southern Gulf of Maine. The Eastern groups move from northern Europe to the Cape Verde Islands. There was no genetic difference between the populations from the Gulf of Maine and Newfoundland but there was a difference when these two groups were compared to the West Indies populations. This study shows that even when there are no actual barriers to individuals moving between groups individuals shows fidelity to certain migration patterns. However, because this is not always the case and animals have been seen to change migration patterns it is suggested that the migration pattern is not imprinted but is fidelity developed when a calf first migrates with its mother. This study shows that the different populations should be managed individually. Genetic results have shown that the Humpback Whale has lost little of its genetic diversity in the years that it was hunted. This is probably because the hunting period was short and the population increased rapidly after the bottleneck. The fact that these Whales are long lived also helps with retaining the genetic diversity though the hunting period, although full recovery of the populations will take at least 50 years. (Image from

5. Using genetics to identify commercial products from endangered species
Molecular genetics can identify species that are endangered and protected but still being bought and sold
Often the products on the market cannot be identified by sight but can be identified using genetics
E.g.. Ivory, horn, shell, meat, feathers, dried leaves
An example of this is seen in the Whale market
The international whaling commission allows a certain amount of whaling for scientific research
These Whales can then be sold to consumers
Often species and geographical source can be identified
Genetics can tell if the products on the market are caught legally or illegally
One use of genetics in conservation is in the identification of illegal trade in endangered species. Often the product cannot be identified by looking at it but can be identified using genetic analysis. Some examples of products that can be identified are, ivory, horn, shell, meat, feathers and dried leaves. An example of this is seen in the Whale market. The international Whaling commission allows the hunting of certain numbers of Whales for “research” and these whales can then be sold to consumers. Studies have been carried out that investigate the species and origin of these products. A spot check of the Japanese market suggests that many whale products are illegal or wrongly labelled.

6. Using genetics to identify commercial products from endangered species 2
Shaving brushes made from Badger hair
Meant to be made from the Hog Badgers (Arctonyx colaris) hair which is an invasive species in Europe
Using molecular genetics the hair of four brushes was found to be from the Eurasian Badger (Meles meles) which is a protected species
In a study by Domingo-Roura et al. (2006) The origins of shavings brushes were questioned. Shaving brushes are made from Badger hair. In Europe there are two Badger species the first is the protected Eurasian Badger (Meles meles) and the second is the invasive Hog Badger (Arctonyx colaris). Using molecular genetics it was found that four of the brushes tested were made from the protected Eurasian Badger.

7. The Cats 3
37 out of 38 species in the felid group are endangered or threatened
Cheetahs (Acinonyx jubatus) have less genomic variation than other cats
The Cheetah’s ancestors underwent a severe reduction in numbers and inbreeding possibly several times or over a long period of time
The Florida Panther has the least genetic variation of any puma sub-species
All these species give us an incite into what happens when genetic diversity decreases which can be put to use in other endangered species
In the felid group there are 38 species, 37 of which are endangered or threatened, the only one that isn't at risk is the domestic cat. When the genetics of species such as the Cheetah are looked into it is shown that there is little genetic diversity and suggests that the Cheetahs went through a reduction in numbers several times or over a long period of time. When this was discovered other members of the cat family were studied and the lions in the Ngorongoro crater in Tanzania, Asiatic lions from the Gir Forest in India and Pumas in Florida all show evidence of a severe population contraction historically. This inbreeding effects the ability of the animals to breed. The Florida panther has the least genetic variation of any of the Puma sub-species and this has resulted in a number of observable effects. 95% of the sperm produced is deformed, there are an increased number of cases of cryptorchidism which is an inherited defect where one or both testicles do not descend. This has gone from zero cases to 80% of the males born in the last 15 years have it. The panthers in Florida are more susceptible to disease than is normal and there is an FIV type virus endemic to the population. All these examples can provide incite into other endangered animals with low population numbers and can give us an idea of what can happen when genetic diversity is dramatically reduced. (Image from

8. The Dogs 4
The Simien Jackal (Canis simensis) is probably the most endangered canid
There are fewer than 500 individuals left and they are in isolated populations
Restricted to the Ethiopian highlands
Habitat loss and fragmentation has restricted the Simien Jackal still more
In one study on the population from the Bale Mountain National Park there was only one mitochondrial genotype found
Another problem is their ability to hybridise with domestic dogs
Habitat destruction and fragmentation are the major threats to the Canids at the moments. One of the species that is in trouble now is the Simien Jackal which is probably the most endangered canid at the moment. There are fewer than 500 individuals left and they exist in isolated populations in the Ethiopian highlands, add to this the impact of habitat destruction and fragmentation and they are even more threatened. In one study on the population from the Bale Mountains it was found that the whole population only had one mitochondrial genotype. These Jackals were also reported to be hybridising with domestic dogs and so further genetic analysis was carried out. When suspected hybrids were tested they had pure Jackal mitochondrial DNA which makes sense as the matings are most probably male dogs and female Jackals. Nine microsatellite loci were tested in the hybrids and alleles that are known from the domestic dog and not the Simien Jackal were found. This shows hybridisation has been occurring and makes it necessary for the domestic dog populations to be controlled not only because of this hybridisation but the dogs also compete for food and transmit canine disease. Rabies is already thought to have killed half of the Simien Jackal population in the Bale Mountains. Maybe the only answer is to try and conserve the remaining genetic diversity ex-situ. (image from

9. The Dogs 4 The Red Wolf (Canis rufus)
Was found in the south central United States
Extinct in the wild since
Single captive population
The origins of the species are questionable
Genetic tests have assisted in making decisions when considering re-introductions
The Red Wolf was found across the south central united states but went extinct in the wild in There is a single captive population that may be reintroduced. It was started with 14 allegedly pure Red Wolves. When the captive breeding colony was initiated genetic samples were taken along with preserved samples from 77 ‘wolves’ from the population they were taken from before they were taken and six Red Wolves that died before One theory is that the Red Wolves diverged from the group before coyotes and Grey Wolves but when the mitochondrial DNA from the Red Wolves is tested it is similar to the Grey Wolves and Coyotes. It is possible that the Red Wolf is a product of several hybridisations between Grey Wolves and Coyotes. What is important is that when the captive Red Wolves are released the effects of hybridisation need to be monitored. When test re-introductions have been carried out male Red Wolves have mated with Coyotes and produced hybrid offspring. Solutions could include re-introducing several Red Wolf packs or removing Coyotes from an area. A larger question is, should the Red Wolf be conserved if it is only a historical hybrid? (Image from Monty Sloan on

10. The Birds 5
The Island of Guam had the brown tree snake introduced and the native species of birds have been in trouble ever since
The Guam Rail (Rallus owstoni) and the Micronesian Kingfisher (Halcyon cinnamomina) are extinct in the wild
Genetic analysis has helped to manage matings by looking at relatedness among the captive birds
The results show low genetic diversity but none of this has been lost since the species have been taken into captivity
An example of using genetics in conservation for avian species is seen on the Island of Guam. The introduction of the brown tree snake put the bird species at risk. Two species of note are the Guam Rail and the Micronesian Kingfisher. These have been taken into captivity and a breeding programme established. Genetic analysis aided in the management of the captive populations as relatedness could be determined and this stopped close relatives being paired. Now the Rails are being reintroduced onto a near by island and genetics is playing a role in which individuals to reintroduce. (Images from wikipedia contributers, “Guam Rail,” Wikipedia the free encyclopedia, accsessed 21st July 2006, Warner, M. P. (2004)

11. Marine Turtles 6
There are seven species alive today and all are endangered or threatened
Molecular genetics has helped establish some natural history and evolution that is beneficial to conservation efforts
As with the Whales discussed earlier Green, Loggerhead and Hawksbill turtles return to the same rookery (egg laying site)
Using genetic analysis this has been shown to be the turtles returning to their beach of birth
There are seven species of marine turtles alive today. All of which are endangered or threatened. Genetics has been essential in forming conservation plans because turtles are morphologically conservative meaning that genetics are needed to uncover phylogenies. Long generations, long migrations and the general habits of the turtles make them difficult to track and study. Three of the turtles, the Green turtle, Loggerhead turtle and the Hawksbill turtle are known to show similar breeding site fidelity as the Whales already mentioned. There are three hypotheses as to why the turtles return to the same beach to breed. The first is that the female turtles are returning to the site they were born at, the second is that first time mothers are shown the way to a breeding site by a more experienced female and the last theory is that first time mothers randomly select a beach and then use that beach every time afterwards. The theory that females are returning to their beach of birth can be tested using genetics. Each rookery should have a distinct female line. Using the Green Turtle, mitochondrial DNA was sampled at 15 turtle rookeries. Most rookeries showed unique mitochondrial DNA genotypes. This result suggests that the turtles are not being taken to sites by more experienced females. To test the hypothesis that turtles are just encountering a beach and laying there, it must be checked that there is not some physical barrier stopping the females choosing any beach. This has been done in the Atlantic- Mediterranean and there is a strong tie between females and their natal site. This information is very important when it comes to turtle conservation. It suggests that these rookeries should be looked at separately and if one rookery is overexploited it will not recover from individuals coming in from other rookeries. For example the Green turtle rookery that existed on Grand Cayman island in the Caribbean was exploited and disappeared and has never been recolonised. (Images from wikipedia contributers, “Green Sea turtle,” Wikipedia the free encyclopedia, accsessed 21st July 2006, wikipedia contributers, “Loggerhead Sea Turtle,” Wikipedia the free encyclopedia, accsessed 21st July 2006, wikipedia contributers, “Harwsbill Turtle,” Wikipedia the free encyclopedia, accsessed 21st July 2006 )

12. Endemic plants 7
Spreading Avens (Geum radiatum) is a perennial herb that is found only on a few mountain tops in North Carolina and Tennessee
In 1991 there were 16 populations
Now there are 11
Extinction is being caused by human trampling
Four of the other populations are declining
The government want to restore the numbers of the plant in one of the declining populations, genetic analysis will help with the answer
So far we have only talked about animals. Endemic plants are also being threatened throughout the world and genetics can help in management plans for them too. One example is found in America in North Carolina and Tennessee. The plant is called spreading Avens and is now only found on a few mountain tops. In 1991 there were 16 populations and now there are only 11. Extinction is mainly caused by hikers trampling the plants. Four of the 11 populations are declining in numbers and the government has decided to restore the numbers at one site of decline. Genetic analysis will show which of the other populations would be best to take propagules from. 5 populations were analysed and genetic diversity was low. The questions that must be asked when deciding to take plants from a source populations are, is the source population going to cope with the removal of propagules? Does the source population contain a representative amount of genetic diversity? And, out of all of the populations which is most similar to the recipient population? Answering these questions by looking at the genetics, two donor populations were found. (Image from Justice, W.

13. Pelagic Fish 8
The Billfish group contains Swordfish, Marlins, Sailfish and Spearfish
These fish are commercially exploited and their numbers have decreased
It was not known if these animals were moving about the sea as distinct populations or whether they were a continuous population
Molecular genetics have been used to find some answers
The Striped and Blue Marlin both show within ocean population differences even though they travel great distances
This should shape future conservation plans
The Billfish group has two families and encompasses the Swordfish, Marlins, Sailfish and Spearfish. These fish are all commercially exploited and their numbers are in decline. Due to the problems with tagging and recapturing these fish it has been difficult to test if these fish form continuous populations or are sub-divided. Molecular genetics have now been used to find some answers. The Striped Marlin is found throughout the Pacific and Indian ocean. Fish have been known to travel 1,000km. Before any genetics were run it was concluded that the Striped Marlin was a single stock. Genetic analysis has shown that there is more than one population. This was also seen in the Blue Marlin. Interestingly the tagging data showed that it was a circumtropical species. This has been refuted by genetic analysis where there was a difference between populations in each of the oceans (Atlantic and Pacific) as well as within ocean population structure. The tagging data shows that these fish move large distances but are still grouped into genetically distinct lines, it is possible that these animals are showing a fidelity to spawning grounds. This is relevant to conservation because if one of these populations were to be lost their unique genetic variation would be lost along with them. Management plans should be constructed in a way that takes into account these small regional stocks. (Images from wikipedia contributers, “Swordfish,” Wikipedia the free encyclopedia, accsessed 21st July 2006, wikipedia contributers, “Marlin,” Wikipedia the free encyclopedia, accsessed 21st July 2006, wikipedia contributers, “Sail Fish,” Wikipedia the free encyclopedia, accsessed 21st July 2006)

14. Komodo Dragons 9 Large reptile
Endemic to 5 islands in South East Indonesia
Threatened by habitat destruction and competition by humans
Genetic diversity of five populations on four of the islands studied
Island of Komodo had the greatest diversity
Island of Komodo has been separated from other land masses for the longest period
Makes Komodo population important to conserve
The Komodo Dragon is a large reptile endemic to 5 islands in the Lesser Sundra region in South East Indonesia. It is threatened by the usual suspects of habitat destruction and fragmentation and competition with humans for prey. The genetic diversity was studied from 5 locations. Over all 117 samples were taken. In all of the populations there was a high degree of variation with the population on Komodo Island having the greatest diversity. The Island of Komodo has been separated from the other land masses for the longest period of time, so with this historical isolation and genetic distinctiveness the population of Komodo Dragons on Komodo need special attention. (Image from wikipedia contributers, “Komodo Dragon,” Wikipedia the free encyclopedia, accsessed 21st July 2006

15. Corroboree Frogs 10
Restricted range in Southern Highlands of New South Wales and the Australian Capital territory
Three geographically isolated populations
Snowy Mountains
Fiery Range
Brindabella Range
Snowy mountain population has decreased heterozygosity and an absence of rare alleles
May cause the population to struggle to respond to climate change
The Corroboree frog comes from the Southern Highlands of New South Wales and the Australian Capital territory. Here is has a very restricted range with three geographically isolated populations, the Snowy Mountain population, the Fiery Range populations and the Brindabella Range. Each of these sites has a number of partially isolated breeding populations. It has been noted that there are morphological differences between the Snowy Mountain frogs and the other two populations. Looking at the three populations genetics, the Snowy Mountain population has a decreased heterozygosity and almost all of the rare alleles that were found in the other two populations are absent from the Snowy Mountain population. The reason for this decreased diversity could be a series of bottlenecks, in fact reports suggest that climatic conditions were not ideal for the Snowy Mountain populations for a number of years. As a result of this low heterozygosity and absence of rare alleles the Snowy Mountain frog populations are susceptible to unforeseen evolutionary pressure and this may alter their ability to respond to environmental change. (Image from

16. References
Baker, C. S. and Palumbi, S. R.(1996) Population structure, Molecular systematics and forensic identification of Whales and Dolphins. In Conservation Genetics: Case Histories From Nature eds. Avise, J. C. and Hamrick, J..pp 10-41
Domingo- Roura, X. et al. (2006). Radger hair in shaving brushes comes from protected Eurasian Badgers. Biological Conservation 128:
O’Brian, S. J. (1996) Conservation Genetics of the Felidae In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J. pp50-71
Wayne, R. K. (1996)Conservation Genetics of the Canidae. In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J. pp
Haig, S. M. and Avise, J. C. (1996) Avian Conservation Genetics. In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J..pp

17. References
Bowen, B. W. and Avise, J. C. (1996) Conservation genetics of marine turtles. In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J..pp
Hamrick, J. L. and Godt, M. J. W. (1996) Conservation genetics of endemic plant species. In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J..pp
Graves, J. E. (1996) Conservation Genetics of Fishes in the Pelagic Marine Realm. In Conservation Genetics, Case Histories From Nature eds. Avise, J. C. and Hamrick, J..pp
Ciofi, et al. (1999). Genetic divergence and units for conservation in the Komodo Dragon Varanus komodoensis. Proceeding of the Royal Society of London B. 266:
Osborne, W. S. and Norman, J. A. (1991). Conservation Denetics of Corroboree frogs, Pseudophryne corroboree More (Anura: Myobatrachidad): Population sub-division and genetic divergence. Australian Journal of Zoology 39: